Align Glucose/galactose porter (characterized)
to candidate Ga0059261_0767 Ga0059261_0767 glucose/galactose transporter
Query= TCDB::P0C105 (412 letters) >lcl|FitnessBrowser__Korea:Ga0059261_0767 Ga0059261_0767 glucose/galactose transporter Length = 434 Score = 376 bits (965), Expect = e-109 Identities = 202/389 (51%), Positives = 258/389 (66%), Gaps = 13/389 (3%) Query: 31 LFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVKRISYKRG 90 LFF++G IT LND++IP LK +F LNYTQ+ML+QFCFF AY ++ +P +LVK++ Y RG Sbjct: 33 LFFIFGGITSLNDVIIPKLKELFTLNYTQAMLVQFCFFTAYLVIGIPGAKLVKKLGYMRG 92 Query: 91 IVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILGKPETAAS 150 V GL+ +GC LFIPA+ Y Y +FL ALFVLASGV I+QV ANP +++LGKPETA S Sbjct: 93 AVAGLLTMMVGCLLFIPASQYATYGVFLFALFVLASGVVIVQVVANPLISLLGKPETAHS 152 Query: 151 RLTLTQAFNSLGTTVAPVFGAVLILSAATDATVN------------AEADAVRFPYLLLA 198 RLT QAFNSLGTTV P+ G++LIL + T + AE+ A+ YL +A Sbjct: 153 RLTFAQAFNSLGTTVFPIVGSILILGSLATVTADQLSGPALEAYRVAESKAIMHGYLGIA 212 Query: 199 LAFTVLAIIFAILKPPDVQEDEPALSDKKEGSAWQYRHLVLGAIGIFVYVGAEVSVGSFL 258 A V+A + + + E A + GA+ IF+YVGAEVS+GS + Sbjct: 213 AALAVVAGVVWLFRNRLKGERHQASAGLAGLDLLGRPRFGFGALCIFLYVGAEVSIGSLI 272 Query: 259 VNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMRYIDDGKALAFNAFVAIILLF 318 VN+L P V GL E A + ++WGGAMVGRFIGS MR I GK LAF A A+ L+ Sbjct: 273 VNYLMQPGVMGLQEQAAGKLIGFYWGGAMVGRFIGSGLMRVISPGKLLAFVAVGAVALIL 332 Query: 319 ITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGILCLAIVGGAIVPLI 378 I+ TTGH+A +S+LAIGL NSIMFPTIFSLA LG + GSGI+ +AI GGA+VPL Sbjct: 333 ISTNTTGHVAGYSLLAIGLMNSIMFPTIFSLASEKLGGRAADGSGIINIAIFGGAVVPLA 392 Query: 379 QGALADAIG-IHLAFLMPIICYAYIAFYG 406 GALADA G + LA ++P ICYA IA +G Sbjct: 393 TGALADATGSLGLALILPAICYAIIAGFG 421 Lambda K H 0.328 0.141 0.420 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 600 Number of extensions: 36 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 412 Length of database: 434 Length adjustment: 32 Effective length of query: 380 Effective length of database: 402 Effective search space: 152760 Effective search space used: 152760 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory